3EWJ

Crystal structure of catalytic domain of TACE with carboxylate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel spirocyclopropyl hydroxamate and carboxylate compounds as TACE inhibitors.

Guo, Z.Orth, P.Wong, S.C.Lavey, B.J.Shih, N.Y.Niu, X.Lundell, D.J.Madison, V.Kozlowski, J.A.

(2009) Bioorg Med Chem Lett 19: 54-57

  • DOI: 10.1016/j.bmcl.2008.11.034
  • Primary Citation of Related Structures:  
    3EWJ

  • PubMed Abstract: 
  • We have discovered nanomolar inhibitors of TNF-alpha convertase (TACE) comprised of a novel spirocyclic scaffold and either a carboxylate or hydroxamate zinc binding moiety. X-ray crystal structures and computer models of selected compounds binding to TACE explain the observed SAR ...

    We have discovered nanomolar inhibitors of TNF-alpha convertase (TACE) comprised of a novel spirocyclic scaffold and either a carboxylate or hydroxamate zinc binding moiety. X-ray crystal structures and computer models of selected compounds binding to TACE explain the observed SAR. We report the first TACE X-ray crystal structure for an inhibitor with a carboxylate zinc ligand.


    Organizational Affiliation

    Department of Chemistry, Schering-Plough Research Institute, Kenilworth, NJ 07033-0539, USA. zhuyan.guo@spcorp.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADAM 17A, B271Homo sapiensMutation(s): 3 
Gene Names: ADAM17CSVPTACE
EC: 3.4.24.86
UniProt & NIH Common Fund Data Resources
Find proteins for P78536 (Homo sapiens)
Explore P78536 
Go to UniProtKB:  P78536
PHAROS:  P78536
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
642 (Subject of Investigation/LOI)
Query on 642

Download Ideal Coordinates CCD File 
F [auth B](1S,3R,6S)-4-oxo-6-{4-[(2-phenylquinolin-4-yl)methoxy]phenyl}-5-azaspiro[2.4]heptane-1-carboxylic acid
C29 H24 N2 O4
BFZXMIUWGSTUAL-ZSOKXDGFSA-N
 Ligand Interaction
INN (Subject of Investigation/LOI)
Query on INN

Download Ideal Coordinates CCD File 
D [auth A]N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide
C19 H37 N5 O5
LMIQCBIEAHJAMZ-GZBFAFLISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
642 PDBBind:  3EWJ Ki: 143 (nM) from 1 assay(s)
Binding MOAD:  3EWJ Ki: 143 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.398α = 90
b = 76.176β = 90
c = 103.565γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
BUSTER-TNTrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2008-10-15 
  • Released Date: 2008-11-18 
  • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Other